Photonic crystals consisting of nano- to micrometer-sized building blocks, such as multiple sorts of colloids, have recently received widespread attention. It remains a challenge, however, to adequately probe the internal crystal structure and the corresponding deformations that inhibit the proper functioning of such materials. It is shown that scanning transmission X-ray microscopy (STXM) can directly reveal the local structure, orientations, and even deformations in polystyrene and silica colloidal crystals with 30-nm spatial resolution. Moreover, STXM is capable of imaging a diverse range of crystals, including those that are dry and inverted, and provides novel insights complementary to information obtained by benchmark confocal fl uorescence and scanning electron microscopy techniques.